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1
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QSAR studies of a number of triazole antifungal alcohols

100%
Nowaczyk A., Modzelewska-Banachiewicz B.
Open Chemistry
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2010
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vol. 8
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issue 2
440-447
EN
The activity of fungicide agents containing a quinazolinone ring was described using the quantitative structure-activity relationship (QSAR) model by applying it to data taken from literature. The title compounds exhibit two important types of activity against certain fungal pathogens, i.e. activity against yeast and activity against filamentous fungi. A correlation between both antifungal activities (e.g. FA(yst) and FA(ff)) and physicochemical parameters such as the logarithm of the n-octanol/water partition coefficient (log P), the polarizability (P), the global minimum energy (TE), the energy difference between the frontier molecular orbital (DELH) and the molar refractivity (MR), was established using multiple linear regression. The molecular descriptors of the antifungal agents were obtained by quantum chemical calculations combined with molecular modeling calculations. Statistical analysis shows that the antifungal activity depends mainly on the calculated partition coefficients, log P, of the compounds. Bi-parametric models reveal that antifungal activity relates linearly to log P and P. [...]
2
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QSAR modeling for lipid peroxidation inhibition potential of flavonoids using topological and structural parameters

100%
Ray S., Sengupta C., Roy K.
Open Chemistry
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2008
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vol. 6
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issue 2
267-276
EN
In the present study, Quantitative Structure-Activity Relationship (QSAR) modeling has been carried out for lipid peroxidation (LPO)-inhibition potential of a set of 27 flavonoids, using structural and topological parameters. For the development of models, three methods were used: (1) stepwise regression, (2) factor analysis followed by multiple linear regressions (FA-MLR) and (3) partial least squares (PLS) analysis. The best equation was obtained from stepwise regression analysis (Q2 = 0.626) considering the leave-oneout prediction statistics. [...]
3
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2-Amino-4-arylthiazole Derivatives as Anti-giardial Agents: Synthesis, Biological Evaluation and QSAR Studies

100%
Mocelo-Castell R., Villanueva-Novelo C., Cáceres-Castillo D., Carballo R. M., Quijano-Quiñones R. F., Quesadas-Rojas M., Cantillo-Ciau Z., Cedillo-Rivera R., Moo-Puc R. E., Moujir L. M., Mena-Rejón G. J.
Open Chemistry
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2015
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vol. 13
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issue 1
EN
A series of seven 2-amino-4-arylthiazoles were prepared following Hantzsch’s modified method under microwave irradiation. A set of 50 derivatives was obtained and the in vitro activity against Giardia intestinalis was evaluated. The results on the biological activity revealed that, in general, the N-(5-bromo-4-aryl-thiazol-2-yl)-acetamide scaffold showed high bioactivity. In particular, compounds 6e (IC50 = 0.39 μM) and 6b (IC50 = 0.87 μM) were found to be more potent than the positive control metronidazole. Citoxicity and acute toxicity tests performed showed low toxicity and high selectivity of the most active compounds (6e SI = 139, 6b SI = 52.3). A QSAR analysis was applied to a data set of 37 obtained 2-amino-4-arylthiazoles derivatives and the best model described a strongly correlation between the anti-giardiasic activity and molecular descriptors as E2M, RDF115m, F10, MATS6v, and Hypnotic-80, with high statistical quality. This finding indicates that N-substituted aminothiazole scaffold should be investigated for the development of highly selective anti-giardial agent.
4
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QSAR modeling of antiradical and antioxidant activities of flavonoids using electrotopological state (E-State) atom parameters

100%
Ray S., Sengupta C., Roy K.
Open Chemistry
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2007
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vol. 5
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issue 4
1094-1113
EN
In the present paper QSAR modeling using electrotopological state atom (E-state) parameters has been attempted to determine the antiradical and the antioxidant activities of flavonoids in two model systems reported by Burda et al. (2001). The antiradical property of a methanolic solution of 1, 1-diphenyl-2-picrylhydrazyl (DPPH) and the antioxidant activity of flavonoids in a β-carotenelinoleic acid were the two model systems studied. Different statistical tools used in this communication are stepwise regression analysis, multiple linear regressions with factor analysis as the preprocessing step for variable selection (FA-MLR) and partial least squares analysis (PLS). In both the activities the best equation is obtained from stepwise regression analysis, considering, both equation statistics and predictive ability (antiradical activity: R 2 = 0.927, Q2 = 0.871 and antioxidant activity: R 2 = 0.901, Q2 = 0.841). [...]
5
Content available remote

QSAR studies of 2-substituted 2,3-dihydro-1h-naphtho[1,8-de]-1,3,2-diazaphosphorine 2-oxides and sulphides

100%
Madhuritha A., Kumar B., Parthasarathy T., Uma V.
Open Chemistry
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2004
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vol. 2
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issue 4
696-702
EN
A quantitative structure activity relationship (QSAR) study of 2-substituted 2,3-dihydro-1H-naphtho[1,8,de]-1,3,2-diazaphosphorine 2-oxides and sulphides (DND), examines the extent of the contribution by various physicochemical parameters with respect to their antimicrobial activity. Simple bivariant regression analysis, based on the least squares method, is applied in order to predict models. The predicted models reveal that the steric factor, MR, is the major contributor influencing antimicrobial activity. Bulky groups at the C-19 (C=0 group) position positively influence the potency of the compounds
6
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Analysis of the co-evolutions of correlations as a tool for QSAR-modeling of carcinogenicity: an unexpected good prediction based on a model that seems untrustworthy

88%
Toropova A., Toropov A., Diaza R., Benfenati E., Gini G.
Open Chemistry
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2011
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vol. 9
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issue 1
165-174
EN
To validate QSAR models an external test set is increasingly used. However the definition of the compounds for the test set is still debated. We studied, co-evolutions of correlations between optimal descriptors and carcinogenicity (pTD50) for the subtraining, calibration, and test set. Weak correlations for the sub-training set are sometimes accompanied by quite good correlations for the external test set. This can be explained in terms of the probability theory and can help define a suitable test set. The simplified molecular input line entry system (SMILES) was used to represent the molecular structure. Correlation weights for calculating the optimal descriptors are related to fragments of the SMILES. The statistical quality of the model is: n=170, r2=0.6638, q2=0.6554, s=0.828, F=331 (sub-training set); n=170, r2=0.6609, r2pred=0.6520, s=0.825, F=331 (calibration set); and n=61, r2=0.7796, r2pred=0.7658, Rm2=0.7448, s=0.563, F=221 (test set). The calculations were done with CORAL software (http://www.insilico.eu/coral/). [...]
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QSAR study of the DPPH· radical scavenging activity of coumarin derivatives and xanthine oxidase inhibition by molecular docking

88%
Razo-Hernández R., Pineda-Urbina K., Velazco-Medel M., Villanueva-García M., Sumaya-Martínez M., Martínez-Martínez F., Gómez-Sandoval Z.
Open Chemistry
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2014
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vol. 12
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issue 10
1067-1080
EN
A Quantitative Structure-Activity Relationship (QSAR) of coumarins by genetic algorithms employing physicochemical, topological, lipophilic and electronic descriptors was performed. We have used experimental antioxidant activities of specific coumarin derivatives against the DPPH· radical molecule. Molecular descriptors such as Randic Path/Walk, hydrophilic factor and chemical hardness were selected to propose a mathematical model. We obtained a linear correlation with R2 = 96.65 and Q LOO2 = 93.14 values. The evaluation of the predictive ability of the model was performed by applying the Q ASYM2, $\hat r^2 $ and Δr m2 methods. Fukui functions were calculated here for coumarin derivatives in order to delve into the mechanics by which they work as primary antioxidants. We also investigated xanthine oxidase inhibition with these coumarins by molecular docking. Our results show that hydrophobic, electrostatic and hydrogen bond interactions are crucial in the inhibition of xanthine oxidase by coumarins.
8
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QSAR modeling of anxiolytic activity taking into account the presence of keto- and enol-tautomers by balance of correlations with ideal slopes

88%
Toropova A., Toropov A., Benfenati E., Gini G., Leszczynska D., Leszczynski J.
Open Chemistry
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2011
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vol. 9
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issue 5
846-854
EN
Optimal descriptors calculated with simplified molecular input line entry system (SMILES) have been examined as a tool for prediction of anxiolytic activity. Descriptors calculated with SMILES (a) of keto-isomers; (b) of enol-isomers; and (c) of both keto-isomers together with enol-isomers have been studied. Three approaches have been compared: 1. classic’ training-test’ system 2. balance of correlations and 3. balance of correlations with ideal slopes. The best statistical characteristics for the external validation set took place for optimal descriptors calculated with SMILES of both keto-form and enol-form (i.e., molecular structure was represented in the format: ’sMILES of keto-form. SMILES of enol-form’) by means of balance of correlations with ideal slopes. The predictive potential of this model was checked with three random splits. [...]
9
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Investigation of 6-fluoroquinolones activity against Mycobacterium tuberculosis using theoretical molecular descriptors: a case study

88%
Minovski N., Jezierska-Mazzarello A., Vračko M., Šolmajer T.
Open Chemistry
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2011
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vol. 9
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issue 5
855-866
EN
A quantitative structure-activity relationship (QSAR) study on a set of 66 structurally-similar 6-fluoroquinolones was performed using a large pool of theoretical molecular descriptors. Ab initio geometry optimizations were carried out to reproduce the geometrical and electronic structure parameters. The resulting molecular structures were confirmed to be minima via harmonic frequency calculations. Obtained atomic charges, HOMO and LUMO energies, orbital electron densities, dipole moment, energy and many other properties served as quantum-chemical descriptors. A multiple linear regression (MLR) technique was applied to generate a linear model for predicting the biological activity, Minimal Inhibitory Concentration (MIC), treated as negative decade logarithm, (pMIC). The heuristic method was used to optimize the model parameters and select the most significant descriptors. The model was tested internally using the CV LOO procedure on the training set and validated against the external validation set. The result (Q 2 ext = 0.7393), which was obtained on an external, previously excluded validation data set, shows the predictive performances of this model (R 2tr = 0.7416, Q 2 tr = 0.6613) in establishing (Q)SAR of 6-fluoroquinolones. This validated model could be proficiently used to design new 6-fluoroquinolones with possible higher activity. [...]
10
Content available remote

Experimental and modelling studies on antifungal compounds

88%
Doble M., Kumar K.
Open Chemistry
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2006
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vol. 4
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issue 3
428-439
EN
Antifungal activity of organic compounds (aromatic, salicylic derivatives, cinnamyl derivatives etc) on Fusarium Rosium (14 compounds) and Aspergillus niger (17 compounds) was studied and QSAR models were developed relating molecular descriptors with the observed activity. Back propagation Neural Network models and single and multiple regression models were tested for predicting the observed activity. The data fit as well as the predictive capability of the neural network models were satisfactory (R2 = 0.84, q2 = 0.73 for Fusarium Rosium and R2 = 0.75, q2 = 0.62 for Aspergillus niger). The descriptors used in the network for the former were X4 (connectivity) and Jhetv (topological); and TIC1 (information) and SPI (topological) for the latter fungus. Antifungal activities of these organic compounds were generally lower against the latter than with the former fungus.
11
Content available remote

QSAR modelling toxicity toward rats of inorganic substances by means of CORAL

88%
Toropova A., Toropov A., Benfenati E., Gini G.
Open Chemistry
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2011
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vol. 9
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issue 1
75-85
EN
CORAL (‘CORrelation And Logic’) is freeware available on the Internet www.insilico.eu/coral The aim of this program is to establish a correlation between an endpoint and descriptors calculated with a simplified molecular input line entry system (SMILES). Three models calculated by CORAL for toxicity towards rat (-pLD50) of inorganic substances (three random splits) have shown that CORAL could be a good tool to model this endpoint. The average statistical characteristics for the CORAL models are the following: n=38, r2=0.8461, q2=0.8298, s=0.273, F=198 (subtraining set); n=37, r2=0.8144, s=0.322, F=154 (calibration set); and n=10, r2=0.8004, Rm (test)2 =0.7815, s=0.240, F=32 (validation set). [...]
12
Content available remote

QSAR of caffeines by similarity cluster prediction

88%
Harsa T., Harsa A., Szefler B.
Open Chemistry
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2014
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vol. 12
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issue 3
365-376
EN
A novel QSAR approach based on correlation weighting and alignment over a hypermolecule that mimics the investigated correlational space was performed on a set of 40 caffeines downloaded from the PubChem database. The best models describing log P and LD50 values of this set of caffeine derivatives were validated against the external test set and in a new predictive model by using clusters of similarity.
13
Content available remote

Density functional studies of the dipole polarizabilities of the linear polyacenes benzene through nonacene

63%
Hinchliffe A., Nikolaidi B., Soscún Machado H.
Open Chemistry
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2005
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vol. 3
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issue 2
361-369
EN
We report Ab Initio studies of the electric dipole polarizability of the linear polyacene series benzene through nonacene. A number of Ab Initio studies were done at different levels of theory for benzene, with all remaining Ab Initio calculations being at the B3LYP/6-311G(2d, 1p)//B3LYP/6-311+G(2d, 1p) level of theory. We find that the NN tensor component shows a constant increment of 20 atomic units per ring. AM1 and QSAR-quality empirical calculations show poor absolute agreement with the Ab Initio results but given excellent statistical correlation coefficients with the Ab Initio values. This implies that the results of such cheaper calculations can be suitably scaled for predictive purposes.
14
Content available remote

Enhancement of molecular polarizabilities by the push-pull mechanism; a DFT study of substituted benzene, furan, thiophene and related molecules

51%
Hinchliffe A., Mkadmh A., Nikolaidi B., Soscún H., Abu-Awwad F.
Open Chemistry
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2006
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vol. 4
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issue 4
743-759
EN
We report Density Functional Theory (DFT) studies of the dipole polarizabilities of benzene, furan and thiophene together with a number of substituted and related systems. All geometries were optimized (and characterized) at the B3LYP/6-311g(2d,1p) level of theory and polarizabilities then calculated with B3LYP/6-311++G(2d,1p). For the R-ring systems we find group polarizabilities in the order R = NO2 ∼ OCH3 ∼ CN ∼ CHO > NH2 > OH > H = 0. For systems R-ring-R, 〈α〉 differs little from the additivity model, with small positive and negative increments. For systems D-ring-A (where D and A are deactivating and activating groups) we find a positive enhancement to 〈α〉 over and above the value expected on the basis of pure additivity for all pairs A and D studied. This enhancement can be increased greatly by extending the length of the conjugated chain to D-ring-CH=CH-ring-A and D-ring-N=N-ring-A systems. Empirical models of polarizability such as AM1 agree badly with the DFT calculations in an absolute sense but give excellent statistical correlation coefficients. Calculated 〈α〉’s also agree well in a statistical sense with the molecular volumes calculated from molecular mechanics force fields Analysis of the results in terms of the π electrons alone is not satisfactory.
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